```
library("igraph")
library("graphsim")
```

##Set up simulated graph

```
graph_edges <- rbind(c("A", "C"), c("B", "C"), c("C", "D"), c("D", "E"), c("D", "F"), c("F", "G"), c("F", "I"), c("H", "I"))
graph <- graph.edgelist(graph_edges, directed = T)
```

##Plotting

`plot_directed`

with default settings uses the `layout.fruchterman.reingold`

as does the default `igraph::graphsim`

.

```
plot(graph)
```

```
plot_directed(graph)
```

`plot_directed`

supports customised layouts and colours:

```
plot_directed(graph, layout = layout.kamada.kawai)
```

```
plot_directed(graph, fill.node = "lightblue", border.node = "royalblue")
```

Colours may also be entered as a vector for each node in `V(graph)`

:

```
names(V(graph))
```

```
## [1] "A" "C" "B" "D" "E" "F" "G" "I" "H"
```

```
colour_vector <- ifelse(names(V(graph)) %in% c("A", "D", "I"), 1, 2)
plot_directed(graph, fill.node = c("lightblue", "grey")[colour_vector], border.node = c("royalblue", "black")[colour_vector])
```

##Arrow customisation

The `state`

parameter controls whether the links are “activating” or “inhibiting”. These may be applied globally as a character or numeric:

###Activating links

- “activating”
- 1
- 0

###Inhibiting links

- “inhibiting”
- -1
- 2

```
plot_directed(graph, state = "activating")
```

```
plot_directed(graph, state = "inhibiting")
```

```
plot_directed(graph, state = 1)
```

```
plot_directed(graph, state = -1)
```

```
plot_directed(graph, state = 0)
```

```
plot_directed(graph, state = 2)
```

#Vectorisation

The state parameter may also apply as a vector to each edge in E(graph) respectively.

```
E(graph)
```

```
## + 8/8 edges from abc5aa9 (vertex names):
## [1] A->C B->C C->D D->E D->F F->G F->I H->I
```

```
plot_directed(graph, state = c(1, 1, -1, -1, 1, -1, 1, -1))
```